<html>
<body style="padding:20px;width:650px;">
<title>Member/Sequence Table</title>
<h2>Member/Sequence Table</h2>

This table is shown when "Show Selected Clusters" is executed from the cluster table,
or when All Sequences is selected (note, if a nucleotide sequence
was in the singleTCW but not translated into a protein with ESTscan, it will not be shown).
<ul> 
<li>Columns can be added/removed using the <b>Select Columns</b> button below the table. 
<li>Columns can
also be rearranged (by dragging the headers) and sorted (by clicking the headers). 
<li>Put the mouse over a column heading in the <b>Select Columns</b> interface, and a full explanation of the column is shown
in the lower left corner.
</ul>

<h3>Functions at the top:</h3>
<table border=0 cellspacing=3>
<tr><td valign="top"><i>Pairwise Alignment</i><td> Perform pairwise (dynamic-programming) 
alignment for all sequences in the table or the selected set (no more than 1000). 

<tr><td valign="top"><i>MUSCLE Alignment</i><td> Run MUSCLE to build a multiple alignment for all 
sequences in the table or for the selected set (no more than 1000). This is not available from the web applet.

<tr><td valign="top"><i>Export</i> <td>Exports the entire table to a tab-delimited file or exports
the table along with the cluster members to a tab-delimited file.

<tr><td valign="top"><i>Copy Table</i><td> Copies to clipboard the entire table.

<tr><td valign="top"><i>Blast</i><td> For selected sequence: Blast the sequence against the whole sequence set.

<tr><td valign="top"><i>View Details</i><td> For selected sequence: See library counts, RPKM values, 
and annotations. Note: only the top 3 annotations for each annoDB are in the multiTCW,
where occassionally there may be 4 is the 'best anno' does not have a rank <= 3 (see Best Hit
description below).

<tr><td valign="top"><i>View Clusters</i><td>For the selected sequence: 
Show table of clusters containing the sequence.

<tr><td valign="top"><i>Copy</i><td>For the selected sequence: Copies the sequence ID or protein sequence.


</table>

<h3>Sequence Columns:</h3>

<i>General</i>
<table border=0 cellspacing="top">
<tr><td valign="top" nowrap>&nbsp;&nbsp;&nbsp;SeqID<td> Sequence ID, from the sTCW project.
<tr><td valign="top" nowrap>&nbsp;&nbsp;&nbsp;#Align<td> If the sequence is a contig from an sTCW assembly, this shows the
number of reads assembled into the contig.
<tr><td valign="top" nowrap>&nbsp;&nbsp;&nbsp;Length<td> Basepairs in the sequence.
<tr><td valign="top" nowrap>&nbsp;&nbsp;&nbsp;Total Count<td> Summed expression for all libraries (un-normalized).
<tr><td valign="top" nowrap>&nbsp;&nbsp;&nbsp;Count List<td> Un-normalized expression counts for each library.
<tr><td valign="top" nowrap>&nbsp;&nbsp;&nbsp;Total RPKM<td> Summed RPKM for all libraries.
<tr><td valign="top" nowrap>&nbsp;&nbsp;&nbsp;RPKM List<td> RPKM values for each library.
</table>

<p>
<i>Best Hit</i>
<br>
The hit with the most best annotation, which is assigned in the viewSingleTCW as follows:
The hit with the best e-value that also satifies one of the following: (1) is a SwissProt hit, or (2) has a good annotation, which means it does not have a phrase like "uncharacterized protein". A SwissProt hit takes priority over a good annotation if the e-value exponent is within 20% of the first good annotation's e-value, e.g at least 1E-16 if the good annotation is 1E-20. 
<table border=0 cellspacing=3>
<tr><td valign="top">&nbsp;&nbsp;&nbsp;hitID<td> The identifier from the database, e.g. the UniProt ID.
<tr><td valign="top">&nbsp;&nbsp;&nbsp;Eval<td> The BLAST hit with the best annotation

<tr><td valign="top">&nbsp;&nbsp;&nbsp;Descript<td> The hit description.
<tr><td valign="top">&nbsp;&nbsp;&nbsp;Species<td> The hit species.
<tr><td valign="top">&nbsp;&nbsp;&nbsp;Type<td> Type of database (i.e. sp for SwissProt and tr for TrEMBL). 
<tr><td valign="top">&nbsp;&nbsp;&nbsp;Tag<td> The tag assigned (e.g. the taxonomy such as 'plants'). 
<tr><td valign="top">&nbsp;&nbsp;&nbsp;Len<td> Length of protein.
</table>
The last 5 values are taken from the first singleTCW that contains the protein as a hit.


<p>
<i>Library RPKM</i>
<br>
Show the RPKM values for each library. 
<p>
<i>Methods</i>
<br>
This section has one column for each clustering method which was performed.
Each column shows the ID of the cluster containing the sequence, if any. 

<p>
<i>Differential Expression</i>
<br>
Shows the DE scores from the individual sTCW projects, if any.
